Merge branch 'refs/heads/development' into feature/dm-1122-enable-pat…

…-token-auth
qbicsoftware · Mar 25, 2024 · 5c8db7e · 5c8db7e
2 parents 2ebdae7 + cdf0151
commit 5c8db7e
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Showing 39 changed files with 129 additions and 214 deletions.
diff --git a/measurement-provider/pom.xml b/measurement-provider/pom.xml
@@ -5,7 +5,7 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>life.qbic</groupId>
-    <artifactId>data-access-server</artifactId>
+    <artifactId>data-download-server</artifactId>
     <version>1.0-SNAPSHOT</version>
   </parent>
 
@@ -27,7 +27,7 @@
         <configuration>
           <archive>
             <manifestEntries>
-              <Automatic-Module-Name>${project.groupId}.data_access.measurement.provider</Automatic-Module-Name>
+              <Automatic-Module-Name>${project.groupId}.data_download.measurement.provider</Automatic-Module-Name>
             </manifestEntries>
           </archive>
         </configuration>

diff --git a/measurement-provider/src/main/java/life/qbic/data_access/measurements/api/FileInfo.java b/measurement-provider/src/main/java/life/qbic/data_access/measurements/api/FileInfo.java
diff --git a/measurement-provider/src/main/java/life/qbic/data_access/measurements/api/Measurement.java b/measurement-provider/src/main/java/life/qbic/data_access/measurements/api/Measurement.java
diff --git a/...rement-provider/src/main/java/life/qbic/data_access/measurements/api/MeasurementData.java b/...rement-provider/src/main/java/life/qbic/data_access/measurements/api/MeasurementData.java
diff --git a/...rovider/src/main/java/life/qbic/data_access/measurements/api/MeasurementDataProvider.java b/...rovider/src/main/java/life/qbic/data_access/measurements/api/MeasurementDataProvider.java
diff --git a/...rement-provider/src/main/java/life/qbic/data_access/measurements/api/MeasurementInfo.java b/...rement-provider/src/main/java/life/qbic/data_access/measurements/api/MeasurementInfo.java
diff --git a/...ata_access/measurements/api/DataFile.java → ...a_download/measurements/api/DataFile.java b/...ata_access/measurements/api/DataFile.java → ...a_download/measurements/api/DataFile.java
@@ -1,4 +1,4 @@
-package life.qbic.data_access.measurements.api;
+package life.qbic.data_download.measurements.api;
 
 import static java.util.Objects.requireNonNull;
 
@@ -7,12 +7,7 @@
 import java.util.StringJoiner;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * A file with data
  */
 public class DataFile {
 

diff --git a/measurement-provider/src/main/java/life/qbic/data_download/measurements/api/FileInfo.java b/measurement-provider/src/main/java/life/qbic/data_download/measurements/api/FileInfo.java
@@ -0,0 +1,8 @@
+package life.qbic.data_download.measurements.api;
+
+/**
+ * Information about a file
+ */
+public record FileInfo(String path, long length, long crc32, long registrationMillis, long lastModifiedMillis) {
+
+}
diff --git a/measurement-provider/src/main/java/life/qbic/data_download/measurements/api/Measurement.java b/measurement-provider/src/main/java/life/qbic/data_download/measurements/api/Measurement.java
@@ -0,0 +1,8 @@
+package life.qbic.data_download.measurements.api;
+
+/**
+ * A measurement
+ */
+public record Measurement(MeasurementId id, MeasurementInfo info, MeasurementData data) {
+
+}
diff --git a/...ment-provider/src/main/java/life/qbic/data_download/measurements/api/MeasurementData.java b/...ment-provider/src/main/java/life/qbic/data_download/measurements/api/MeasurementData.java
@@ -0,0 +1,10 @@
+package life.qbic.data_download.measurements.api;
+
+import java.io.InputStream;
+
+/**
+ * Measurement data
+ */
+public interface MeasurementData {
+  InputStream stream();
+}
diff --git a/...vider/src/main/java/life/qbic/data_download/measurements/api/MeasurementDataProvider.java b/...vider/src/main/java/life/qbic/data_download/measurements/api/MeasurementDataProvider.java
@@ -0,0 +1,10 @@
+package life.qbic.data_download.measurements.api;
+
+/**
+ * Provides measurement data given a measurement
+ */
+public interface MeasurementDataProvider {
+
+  MeasurementData loadData(MeasurementId measurementId);
+
+}
diff --git a/...asurements/api/MeasurementDataReader.java → ...asurements/api/MeasurementDataReader.java b/...asurements/api/MeasurementDataReader.java → ...asurements/api/MeasurementDataReader.java
@@ -1,14 +1,9 @@
-package life.qbic.data_access.measurements.api;
+package life.qbic.data_download.measurements.api;
 
 import java.io.InputStream;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * Reads measurement data
  */
 public interface MeasurementDataReader extends AutoCloseable {
 

diff --git a/...s/measurements/api/MeasurementFinder.java → ...d/measurements/api/MeasurementFinder.java b/...s/measurements/api/MeasurementFinder.java → ...d/measurements/api/MeasurementFinder.java
@@ -1,4 +1,4 @@
-package life.qbic.data_access.measurements.api;
+package life.qbic.data_download.measurements.api;
 
 public interface MeasurementFinder {
   MeasurementInfo findById(MeasurementId measurementId);

diff --git a/...ccess/measurements/api/MeasurementId.java → ...nload/measurements/api/MeasurementId.java b/...ccess/measurements/api/MeasurementId.java → ...nload/measurements/api/MeasurementId.java
@@ -1,4 +1,4 @@
-package life.qbic.data_access.measurements.api;
+package life.qbic.data_download.measurements.api;
 
 /**
  * The ID of a measurement.

diff --git a/...ment-provider/src/main/java/life/qbic/data_download/measurements/api/MeasurementInfo.java b/...ment-provider/src/main/java/life/qbic/data_download/measurements/api/MeasurementInfo.java
@@ -0,0 +1,8 @@
+package life.qbic.data_download.measurements.api;
+
+/**
+ * Information about a measurement
+ */
+public record MeasurementInfo(long size, int fileCount) {
+
+}
diff --git a/measurement-provider/src/main/java/module-info.java b/measurement-provider/src/main/java/module-info.java
@@ -1,3 +1,3 @@
-module life.qbic.data_access.measurements {
-  exports life.qbic.data_access.measurements.api;
+module life.qbic.data_download.measurements {
+  exports life.qbic.data_download.measurements.api;
 }
diff --git a/openbis-connector/pom.xml b/openbis-connector/pom.xml
@@ -8,7 +8,7 @@
 
   <parent>
     <groupId>life.qbic</groupId>
-    <artifactId>data-access-server</artifactId>
+    <artifactId>data-download-server</artifactId>
     <version>1.0-SNAPSHOT</version>
   </parent>
 
@@ -87,7 +87,7 @@
         <configuration>
           <archive>
             <manifestEntries>
-              <Automatic-Module-Name>${project.groupId}.data_access.openbis.connector</Automatic-Module-Name>
+              <Automatic-Module-Name>${project.groupId}.data_download.openbis.connector</Automatic-Module-Name>
             </manifestEntries>
           </archive>
         </configuration>

diff --git a/openbis-connector/src/main/java/deactivated.module-info.java b/openbis-connector/src/main/java/deactivated.module-info.java
@@ -1,5 +1,5 @@
-//import life.qbic.data_access.measurements.api.MeasurementDataReader;
-//import life.qbic.data_access.openbis.DatasetFileStreamReaderImpl;
+//import life.qbic.data_download.measurements.api.MeasurementDataReader;
+//import life.qbic.data_download.openbis.DatasetFileStreamReaderImpl;
 //
 ///**
 // * TODO!
@@ -9,8 +9,8 @@
 // *
 // * @since <version tag>
 // */
-//module life.qbic.data_access.openbis {
-//  requires life.qbic.data_access.measurements;
+//module life.qbic.data_download.openbis {
+//  requires life.qbic.data_download.measurements;
 //  requires spring.context;
 //  requires spring.beans;
 //  requires org.slf4j;

diff --git a/.../life/qbic/data_access/openbis/ApiV3.java → ...ife/qbic/data_download/openbis/ApiV3.java b/.../life/qbic/data_access/openbis/ApiV3.java → ...ife/qbic/data_download/openbis/ApiV3.java
@@ -1,19 +1,17 @@
-package life.qbic.data_access.openbis;
+package life.qbic.data_download.openbis;
 
 import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
 import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
 import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * A provider for openbis apis v3
  */
 public class ApiV3 {
 
+  private ApiV3() {
+    //hide the implicit constructor
+  }
   public static IApplicationServerApi applicationServer(String url) {
     return HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, url + IApplicationServerApi.SERVICE_URL, 100_000L);
   }

diff --git a/.../openbis/DatasetFileStreamReaderImpl.java → .../openbis/DatasetFileStreamReaderImpl.java b/.../openbis/DatasetFileStreamReaderImpl.java → .../openbis/DatasetFileStreamReaderImpl.java
@@ -1,22 +1,17 @@
-package life.qbic.data_access.openbis;
+package life.qbic.data_download.openbis;
 
 import static java.util.Objects.nonNull;
 
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.DataStore;
 import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownload;
 import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadReader;
 import java.io.InputStream;
-import life.qbic.data_access.measurements.api.DataFile;
-import life.qbic.data_access.measurements.api.FileInfo;
-import life.qbic.data_access.measurements.api.MeasurementDataReader;
+import life.qbic.data_download.measurements.api.DataFile;
+import life.qbic.data_download.measurements.api.FileInfo;
+import life.qbic.data_download.measurements.api.MeasurementDataReader;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * Reads openbis data streams
  */
 public class DatasetFileStreamReaderImpl implements MeasurementDataReader {
 

diff --git a/...data_access/openbis/OpenBisConnector.java → ...ta_download/openbis/OpenBisConnector.java b/...data_access/openbis/OpenBisConnector.java → ...ta_download/openbis/OpenBisConnector.java
@@ -1,4 +1,4 @@
-package life.qbic.data_access.openbis;
+package life.qbic.data_download.openbis;
 
 import static java.util.Objects.requireNonNull;
 import static java.util.function.Predicate.not;
@@ -20,23 +20,18 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.stream.Collectors;
-import life.qbic.data_access.measurements.api.MeasurementData;
-import life.qbic.data_access.measurements.api.MeasurementDataProvider;
-import life.qbic.data_access.measurements.api.MeasurementFinder;
-import life.qbic.data_access.measurements.api.MeasurementId;
-import life.qbic.data_access.measurements.api.MeasurementInfo;
-import life.qbic.data_access.openbis.SessionFactory.OpenBisSession;
+import life.qbic.data_download.measurements.api.MeasurementData;
+import life.qbic.data_download.measurements.api.MeasurementDataProvider;
+import life.qbic.data_download.measurements.api.MeasurementFinder;
+import life.qbic.data_download.measurements.api.MeasurementId;
+import life.qbic.data_download.measurements.api.MeasurementInfo;
+import life.qbic.data_download.openbis.SessionFactory.OpenBisSession;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Component;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * A connector to the openBIS system.
  */
 @Component("openbisConnector")
 public class OpenBisConnector implements MeasurementFinder, MeasurementDataProvider {

diff --git a/...c/data_access/openbis/SessionFactory.java → ...data_download/openbis/SessionFactory.java b/...c/data_access/openbis/SessionFactory.java → ...data_download/openbis/SessionFactory.java
@@ -1,4 +1,4 @@
-package life.qbic.data_access.openbis;
+package life.qbic.data_download.openbis;
 
 import static java.util.Objects.requireNonNull;
 import static org.slf4j.LoggerFactory.getLogger;
@@ -10,12 +10,7 @@
 import org.springframework.stereotype.Service;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * Creates openbis sessions
  */
 @Service("openbisSessionFactory")
 public class SessionFactory {

diff --git a/...ss/openbis/UnspecificMeasurementData.java → ...ad/openbis/UnspecificMeasurementData.java b/...ss/openbis/UnspecificMeasurementData.java → ...ad/openbis/UnspecificMeasurementData.java
@@ -1,15 +1,11 @@
-package life.qbic.data_access.openbis;
+package life.qbic.data_download.openbis;
 
 import java.io.InputStream;
-import life.qbic.data_access.measurements.api.MeasurementData;
+import life.qbic.data_download.measurements.api.MeasurementData;
 
 /**
- * TODO!
- * <b>short description</b>
- *
- * <p>detailed description</p>
- *
- * @since <version tag>
+ * A default implementation of {@link MeasurementData}. No specific type of measurement but can be
+ * streamed.
  */
 public class UnspecificMeasurementData implements MeasurementData {
 

diff --git a/...nbis/DatasetFileStreamReaderImplTest.java → ...nbis/DatasetFileStreamReaderImplTest.java b/...nbis/DatasetFileStreamReaderImplTest.java → ...nbis/DatasetFileStreamReaderImplTest.java
@@ -1,4 +1,4 @@
-package life.qbic.data_access.openbis;
+package life.qbic.data_download.openbis;
 
 import static org.junit.jupiter.api.Assertions.*;
 

diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
   <modelVersion>4.0.0</modelVersion>
 
   <groupId>life.qbic</groupId>
-  <artifactId>data-access-server</artifactId>
+  <artifactId>data-download-server</artifactId>
   <version>1.0-SNAPSHOT</version>
   <packaging>pom</packaging>
   <modules>

diff --git a/rest-api/src/main/java/deactivated.module-info.java b/rest-api/src/main/java/deactivated.module-info.java
@@ -1,7 +1,7 @@
 /*
 * as long as not all dependencies are modularized, this needs to open itself to the unnamed package.
  */
-//module life.qbic.data_access.rest {
+//module life.qbic.data_download.rest {
 //  requires spring.boot;
 //  requires spring.boot.autoconfigure;
 //  requires spring.web;